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Error when using 10mer peptide as a input #7

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croshong opened this issue Apr 30, 2020 · 0 comments
Open

Error when using 10mer peptide as a input #7

croshong opened this issue Apr 30, 2020 · 0 comments

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@croshong
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Hi my name is Jong hui Hong

I'm now trying to predict the binding between my peptide seq and mhc

It works well when the length of peptide is 9

But when peptide length was 10

It throws error like this

0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/awork10-3/DeepLigand/elmo_embed.py", line 72, in
context_ids = batcher.batch_sentences(tokenized_context, max_length=args.max_len)
TypeError: batch_sentences() got an unexpected keyword argument 'max_length'
data embedding
running python /awork10-3/DeepLigand/embed_plusrelation_elmo_massspec.py --mhcfile /awork10-3/DeepLigand/output_x/test.mhc --pepfile /awork10-3/DeepLigand/output_x/test.pep.padded --labelfile /awork10-3/DeepLigand/output_x/test.label --relationfile /awork10-3/DeepLigand/output_x/test.relation --masslabelfile /awork10-3/DeepLigand/output_x/test.masslabel --elmodir /awork10-3/DeepLigand/output_x/test.pep.token --elmotag elmo_embeddingds_alltrain.epitope.elmo --mapper /awork10-3/DeepLigand/data/onehot_first20BLOSUM50 --outfileprefix /awork10-3/DeepLigand/output_x/test.h5.batch --expected_pep_len 9
Traceback (most recent call last):
File "/awork10-3/DeepLigand/embed_plusrelation_elmo_massspec.py", line 107, in
embed_all(f1, f2, f3, f4, f5, args.elmodir, args.elmotag, mapper, args.outfileprefix)
File "/awork10-3/DeepLigand/embed_plusrelation_elmo_massspec.py", line 52, in embed_all
assert(exists(join(elmo_dir, 'batch'+str(elmo_cnt)+'.'+elmotag+'.hdf5')))
AssertionError

When I see the training data and example, I think there is no reason that peptide with 10mer
is not working at all
Can somebody suggest me what kind of mistake I made ?

Thanking in advance

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